The nuclear factor kappa B (NF-kB) family of transcription factors controls inter- and intracellular signaling, cellular stress responses, cell growth, survival, and apoptosis. In resting cells, NF-kB dimers with transcription activation potential are sequestered in the cytoplasm by interaction with a family of inhibitors of kappa B proteins (lkBs). Following the action of a large number of different stimuli, the inhibitor is phosphorylated, ubiquinated, and degraded, freeing the NF-kB nuclear localization signal which targets the NF-kB to the nucleus. Differential transcription activation of target genes is linked to temporal control of NF-kB activity that can be described by a mathematical model. In Overall AIM 1, we will explore the dynamics of the interaction between the NF-kB transcription factors and their inhibitors. Binding kinetics and thermodynamics for the lkBalpha /NF-kB interaction will be correlated to theoretical predictions of whether and where folding is coupled to binding in the interaction. New structures of the complexes formed between family members will be solved and dynamics changes that occur upon complex formation will be analyzed. The experiments will better parameterize the mathematical model. In Overall AIM 2, we will explore the structure and function of free lkBalpha and endeavor to understand whether its partially folded structure is important for any of its functions. Free lkBalpha has marginal in vitro thermodynamic stability and may be degraded intracellularly by a ubiquitin-independent proteasome degradation pathway. A panel of mutants will be analyzed for thermodynamic stability and in vitro and in vivo proteasome degradation rates. In Overall AIM 3, we will develop novel integrative approaches that cross the boundaries from in silico theory to in vitro biochemical and biophysical experiments to the in vivo properties of the NF-kB signaling network. Theoretical algorithms will be developed to more accurately predict structures from low resolution experimental data on partially folded protein ensembles. Our unique combination of theory, in vitro biochemical and biophysical characterization, and in vivo studies will enable us to map the landscape by systematic perturbation of the NF-kB signaling network. Thus, the NF-kB/lkBalpha signaling system represents a unique example where a deep biophysical understanding of the protein interaction dynamics can be quantitatively linked to the emergent biological response.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
3P01GM071862-04S1
Application #
7924964
Study Section
Special Emphasis Panel (ZRG1-BCMB-F (41))
Program Officer
Wehrle, Janna P
Project Start
2009-09-30
Project End
2011-03-31
Budget Start
2009-09-30
Budget End
2011-03-31
Support Year
4
Fiscal Year
2009
Total Cost
$127,463
Indirect Cost
Name
University of California San Diego
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
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Narang, Dominic; Chen, Wei; Ricci, Clarisse G et al. (2018) RelA-Containing NF?B Dimers Have Strikingly Different DNA-Binding Cavities in the Absence of DNA. J Mol Biol 430:1510-1520
Wang, Zhipeng; Potoyan, Davit A; Wolynes, Peter G (2018) Modeling the therapeutic efficacy of NF?B synthetic decoy oligodeoxynucleotides (ODNs). BMC Syst Biol 12:4
Ramsey, Kristen M; Narang, Dominic; Komives, Elizabeth A (2018) Prediction of the presence of a seventh ankyrin repeat in I?B? from homology modeling combined with hydrogen-deuterium exchange mass spectrometry (HDX-MS). Protein Sci 27:1624-1635
Wang, Zhipeng; Potoyan, Davit A; Wolynes, Peter G (2018) Stochastic resonances in a distributed genetic broadcasting system: the NF?B/I?B paradigm. J R Soc Interface 15:
Ramirez-Sarmiento, Cesar A; Komives, Elizabeth A (2018) Hydrogen-deuterium exchange mass spectrometry reveals folding and allostery in protein-protein interactions. Methods 144:43-52
Dembinski, Holly E; Wismer, Kevin; Vargas, Jesse D et al. (2017) Functional importance of stripping in NF?B signaling revealed by a stripping-impaired I?B? mutant. Proc Natl Acad Sci U S A 114:1916-1921
Potoyan, Davit A; Bueno, Carlos; Zheng, Weihua et al. (2017) Resolving the NF?B Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors. J Am Chem Soc 139:18558-18566
Potoyan, Davit A; Wolynes, Peter G (2017) Stochastic dynamics of genetic broadcasting networks. Phys Rev E 96:052305
Ramsey, Kristen M; Dembinski, Holly E; Chen, Wei et al. (2017) DNA and I?B? Both Induce Long-Range Conformational Changes in NF?B. J Mol Biol 429:999-1008

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